Modeling Biomolecular Systems II

Biology 5477 / Biomedical Engineering 540

Fall Term 2004

Coursemaster: David Sept

General Information

Syllabus & Schedule [PDF]

Lecture Summaries

Lecture 1 (September 2): Introduction - Dave's Philosophy of Simulations [PDF]

Lecture 3 (September 9): Basics of Biomolecular Structure [PDF]

Lecture 4 (September 14): Potential Energy Surfaces [PDF]

Lecture 5 (September 16): Force Fields and Molecular Mechanics [PDF]

Lecture 6 (September 21): Introduction to QM Calculations [PDF]

Lecture 7 (September 23): Parameterization of a Polarizable Force Field [PDF]

Lecture 22 (November 16): Free Energy Calculations: Methodology [PDF]

Lecture 23 (November 18): Free Energy Calculations: Applications [PDF]

Handouts & Reading

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and
Organic Molecules, W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz,
D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman,
J. Am. Chem. Soc., 117, 5179-5197 (1995) [PDF]

How Well Does a Restrained Electrostatic Potential (RESP) Model Perform
in Calculating Conformational Energies of Organic and Biological Molecules?,
J. Wang, P. Cieplak and P. A. Kollman
J. Comput. Chem., 21, 1049-1074 (2000) [PDF]

Free Energy Calculations: The Long and Winding Gilded Road,
C. Chipot and D. A. Pearlman
Molecular Simulation, 28, 1-12 (2002) [PDF]